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Stacking Interactions and DNA Intercalation

S Li ; VR Cooper ; Timo Thonhauser ; Bengt I. Lundqvist (Institutionen för teknisk fysik, Material- och ytteori) ; D. C. Langreth
Journal of Physical Chemistry B (1520-6106). Vol. 113 (2009), 32, p. 11166.
[Artikel, refereegranskad vetenskaplig]

The relationship between stacking interactions and the intercalation of proflavine and ellipticine within DNA is investigated using a nonempirical van der Waals density functional for the correlation energy. Our results, employing a binary stack model, highlight fundamental, qualitative differences between base-pair-base-pair interactions and that of the stacked intercalator-base-pair system. The most notable result is the paucity of torque, which so distinctively defines the twist of DNA. Surprisingly, this model, when combined with a constraint on the twist of the surrounding base-pair steps to match the observed unwinding of the sugar-phosphate backbone, was sufficient for explaining the experimentally observed proflavine intercalator configuration. Our extensive mapping of the potential energy surface of base-pair-intercalator interactions call provide valuable information for future nonempirical studies of DNA intercalation dynamics.



Denna post skapades 2010-01-14. Senast ändrad 2013-10-29.
CPL Pubid: 107541

 

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Institutioner (Chalmers)

Institutionen för teknisk fysik, Material- och ytteori (1900-2015)

Ämnesområden

Makromolekylfysik

Chalmers infrastruktur